Can i transfer my share from kotak demat to zerodha demat account? Would i be facing any kind of issues further in terms of selling shares in the futures?

There shouldn’t be a problem in this. Its a fairly normal thing to do.

You’ll have to initiate an ‘off market transfer’ from your Kotak Demat account to Zerodha Demat by filling in the DIS slip issued to you by Kotak. The filled DIS will have to be submitted to Kotak along with a copy of your Client master report issued to you by Zerodha.

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On transferring as above, does stock exchange (NSE to BSE) will also change from that of buying in Kotak’s Demat account to Zerodha account?

Kishan, shares in your Demat account aren’t mapped to any specific exchange, you can sell this on any exchange you wish to. This post will help you understand it better.

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Thanks for the help.
Does selling on another exchange will have any additional charges?

No, there are no additional charges. You can calculate charges for both exchanges here.